CPSP - Constraint-based Protein Structure Prediction

This document provides reference information about the Constraint-based Protein Structure Prediction Approach of Rolf Backofen and Sebastian Will.

Version 2.3.1

The goal

This C++ programming library provides fast and easy extensible implementation of the constraint-based approach of Rolf Backofen and Sebastian Will to predict proven optimal structures of simplified 3D-lattice proteins in the HP-model.

Furthermore it will collect additional tools related to this.

CPSP Library Features

• A set of tools for direct 3D-lattice HP-model concerning tasks
• Full library implementation of the CPSP approach of R. Backofen and S. Will
• Interfacing classes to access H-core databases
• Complete API for all classes etc.

Included Tools in 2.3.1

• HPstruct - 3D-lattice structure prediction
• HPstructSC - structure prediction in side chain models
• HPdeg - 3D-lattice degeneracy prediction
• HPoptdeg - Search for low degenerated HP-sequences
• HPoptdegSC - Search for low degenerated HP-sequences
• HPdesign - HP-sequence design for a given structure
• HPnnet - Neutral nets of HP-sequences
• HPrand - Random HP-sequence generation
• HPcompress - HP-sequence (de-)compression
• HPconvert - Lattice structure representation conversion
• HPview - HP lattice protein visualization
• HPviewSC - HP side chain lattice protein visualization

Dependencies

The CPSP depends on the following libraries:

• the Bioinformatic Utility library (BIU) (version 1.3.0)
• the Gecode Constraint Programming Library (version 1.3.0)

Additionally, the documentation also features the following parts:

• Installation

The following lists and indices are available

• List of all classes including brief documentation
• List of all namespaces including brief documentation
• List of all files
• Class hierarchy
• Alphabetical class index
• Namespace members
• Class members
• File members

Contact : http://www.bioinf.uni-freiburg.de/